{"id":"https://openalex.org/W2057445270","doi":"https://doi.org/10.1109/cdc.2013.6760077","title":"Flexible refinement of protein-ligand docking on manifolds","display_name":"Flexible refinement of protein-ligand docking on manifolds","publication_year":2013,"publication_date":"2013-12-01","ids":{"openalex":"https://openalex.org/W2057445270","doi":"https://doi.org/10.1109/cdc.2013.6760077","mag":"2057445270","pmid":"https://pubmed.ncbi.nlm.nih.gov/24830567"},"language":"en","primary_location":{"id":"doi:10.1109/cdc.2013.6760077","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cdc.2013.6760077","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"52nd IEEE Conference on Decision and Control","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4019453","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027625983","display_name":"Hanieh Mirzaei","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hanieh Mirzaei","raw_affiliation_strings":["Division of Systems Eng., Boston University, hanieh@bu.edu","Div. of Syst. Eng., Boston Univ., Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Systems Eng., Boston University, hanieh@bu.edu","institution_ids":["https://openalex.org/I111088046"]},{"raw_affiliation_string":"Div. of Syst. Eng., Boston Univ., Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Elizabeth Villar","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]},{"id":"https://openalex.org/I4210146567","display_name":"Britannia University","ror":"https://ror.org/05gmmwe91","country_code":"BD","type":"education","lineage":["https://openalex.org/I4210146567"]}],"countries":["BD","US"],"is_corresponding":false,"raw_author_name":"Elizabeth Villar","raw_affiliation_strings":["Dept, of Chemistry, Boston University, eavillar@bu.edu","Dept. of Chem., Boston Univ., Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept, of Chemistry, Boston University, eavillar@bu.edu","institution_ids":["https://openalex.org/I111088046","https://openalex.org/I4210146567"]},{"raw_affiliation_string":"Dept. of Chem., Boston Univ., Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019826055","display_name":"Scott E. Mottarella","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Scott Mottarella","raw_affiliation_strings":["Dept, of Bioinformatics, Boston University, semottar@bu.edu","Div. of Syst. Eng., Boston Univ., Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept, of Bioinformatics, Boston University, semottar@bu.edu","institution_ids":["https://openalex.org/I111088046"]},{"raw_affiliation_string":"Div. of Syst. Eng., Boston Univ., Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005150199","display_name":"Dmitri Beglov","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]},{"id":"https://openalex.org/I53560885","display_name":"Orano (United States)","ror":"https://ror.org/04eb8df09","country_code":"US","type":"company","lineage":["https://openalex.org/I4210155143","https://openalex.org/I53560885"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dmitri Beglov","raw_affiliation_strings":["D. Kozakov, D. Beglov, and S. Vajda are with the Dept. of Biomedical Eng., Boston University, midas, dbeglov, vajda@bu.edu","Dept. of Biomed. Eng., Boston Univ., Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D. Kozakov, D. Beglov, and S. Vajda are with the Dept. of Biomedical Eng., Boston University, midas, dbeglov, vajda@bu.edu","institution_ids":["https://openalex.org/I53560885"]},{"raw_affiliation_string":"Dept. of Biomed. Eng., Boston Univ., Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075696701","display_name":"Ioannis Ch. Paschalidis","orcid":"https://orcid.org/0000-0002-3343-2913"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ioannis Ch. Paschalidis","raw_affiliation_strings":["Dept. of Electrical & Computer Eng., and Division of Systems Eng., Boston University, 8 Mary's St., Boston, MA 02215, yannisp@bu.edu","Dept. of Electr. & Comput. Eng., Boston Univ., Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Electrical & Computer Eng., and Division of Systems Eng., Boston University, 8 Mary's St., Boston, MA 02215, yannisp@bu.edu","institution_ids":["https://openalex.org/I111088046"]},{"raw_affiliation_string":"Dept. of Electr. & Comput. Eng., Boston Univ., Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032985635","display_name":"S\u00e1ndor Vajda","orcid":"https://orcid.org/0000-0003-1540-8220"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]},{"id":"https://openalex.org/I53560885","display_name":"Orano (United States)","ror":"https://ror.org/04eb8df09","country_code":"US","type":"company","lineage":["https://openalex.org/I4210155143","https://openalex.org/I53560885"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sandor Vajda","raw_affiliation_strings":["D. Kozakov, D. Beglov, and S. Vajda are with the Dept. of Biomedical Eng., Boston University, midas, dbeglov, vajda@bu.edu","Dept. of Biomed. Eng., Boston Univ., Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D. Kozakov, D. Beglov, and S. Vajda are with the Dept. of Biomedical Eng., Boston University, midas, dbeglov, vajda@bu.edu","institution_ids":["https://openalex.org/I53560885"]},{"raw_affiliation_string":"Dept. of Biomed. Eng., Boston Univ., Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060147489","display_name":"Dima Kozakov","orcid":"https://orcid.org/0000-0003-0464-4500"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]},{"id":"https://openalex.org/I53560885","display_name":"Orano (United States)","ror":"https://ror.org/04eb8df09","country_code":"US","type":"company","lineage":["https://openalex.org/I4210155143","https://openalex.org/I53560885"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dima Kozakov","raw_affiliation_strings":["D. Kozakov, D. Beglov, and S. Vajda are with the Dept. of Biomedical Eng., Boston University, midas, dbeglov, vajda@bu.edu","Dept. of Biomed. Eng., Boston Univ., Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D. Kozakov, D. Beglov, and S. Vajda are with the Dept. of Biomedical Eng., Boston University, midas, dbeglov, vajda@bu.edu","institution_ids":["https://openalex.org/I53560885"]},{"raw_affiliation_string":"Dept. of Biomed. Eng., Boston Univ., Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002097523","display_name":"Pirooz Vakili","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pirooz Vakili","raw_affiliation_strings":["Division of Systems Eng., Boston University, hanieh@bu.edu","Dept. of Mech. Eng., Boston Univ., Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Systems Eng., Boston University, hanieh@bu.edu","institution_ids":["https://openalex.org/I111088046"]},{"raw_affiliation_string":"Dept. of Mech. Eng., Boston Univ., Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":3.0547,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.90774203,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"65","issue":null,"first_page":"1392","last_page":"1397"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9955999851226807,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9955999851226807,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9889000058174133,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11041","display_name":"Ubiquitin and proteasome pathways","score":0.9804999828338623,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.7205249667167664},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.7186275720596313},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6038147807121277},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3728325366973877},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.19548550248146057},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.1636207401752472},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.15373018383979797}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7205249667167664},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.7186275720596313},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6038147807121277},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3728325366973877},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.19548550248146057},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.1636207401752472},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.15373018383979797},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1109/cdc.2013.6760077","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cdc.2013.6760077","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"52nd IEEE Conference on Decision and Control","raw_type":"proceedings-article"},{"id":"pmid:24830567","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24830567","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the ... IEEE Conference on Decision & Control. IEEE Conference on Decision & Control","raw_type":null},{"id":"pmh:oai:europepmc.org:2997605","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC4019453","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:4019453","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4019453","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc IEEE Conf Decis Control","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:4019453","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4019453","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc IEEE Conf Decis Control","raw_type":"Text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.8299999833106995}],"awards":[{"id":"https://openalex.org/G700947639","display_name":null,"funder_award_id":"R01-GM061867","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G748954555","display_name":null,"funder_award_id":"R01 GM093147","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1493390473","https://openalex.org/W1923779967","https://openalex.org/W1965410913","https://openalex.org/W1970845222","https://openalex.org/W1997084106","https://openalex.org/W2026247887","https://openalex.org/W2051434435","https://openalex.org/W2052789270","https://openalex.org/W2064053868","https://openalex.org/W2091734240","https://openalex.org/W2097281366","https://openalex.org/W2103994532","https://openalex.org/W2105668062","https://openalex.org/W2116211618","https://openalex.org/W2127594538","https://openalex.org/W2130479394","https://openalex.org/W2150399099","https://openalex.org/W2162166182","https://openalex.org/W4205293427","https://openalex.org/W4243603320","https://openalex.org/W4253973328","https://openalex.org/W6640156344"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W4391375266","https://openalex.org/W1581147483","https://openalex.org/W4310018788","https://openalex.org/W4398796548","https://openalex.org/W2329052364","https://openalex.org/W2162967120","https://openalex.org/W1567411871","https://openalex.org/W2553094381","https://openalex.org/W2072180710"],"abstract_inverted_index":{"Our":[0,85],"work":[1],"is":[2,67,101],"motivated":[3],"by":[4],"energy":[5],"minimization":[6,31,112],"of":[7,28,71,105],"biological":[8],"macromolecules,":[9],"an":[10,33,60,103],"essential":[11],"step":[12],"in":[13],"computational":[14,86,115],"docking.":[15,118],"By":[16],"allowing":[17],"some":[18],"ligand":[19],"flexibility,":[20],"we":[21],"generalize":[22],"a":[23,63,89],"recently":[24],"introduced":[25],"novel":[26],"representation":[27],"rigid":[29],"body":[30],"as":[32,59],"optimization":[34,61,91],"on":[35,40,62,95],"the":[36,41,51,68,109],"SO(3)\u00d7\u211d3manifold,":[37],"rather":[38],"than":[39,108],"commonly":[42],"used":[43],"Special":[44],"Euclidean":[45],"group":[46,65],"SE(3).":[47],"We":[48],"show":[49,98],"that":[50,66,99],"resulting":[52],"flexible":[53],"docking":[54],"can":[55,81],"also":[56],"be":[57,82],"formulated":[58],"Lie":[64,73],"direct":[69],"product":[70],"simpler":[72],"groups":[74],"for":[75,88,114],"which":[76],"geodesics":[77],"and":[78],"exponential":[79],"maps":[80],"easily":[83],"obtained.":[84],"results":[87],"local":[90,111],"algorithm":[92],"developed":[93],"based":[94],"this":[96],"formulation":[97],"it":[100],"about":[102],"order":[104],"magnitude":[106],"faster":[107],"state-of-the-art":[110],"algorithms":[113],"protein-small":[116],"molecule":[117]},"counts_by_year":[{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":2}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
